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Genome-Wide Survey and Development of the First Microsatellite Markers Database ( AnCorDB) in Anemone coronaria L. Int J Mol Sci 2022; 23:ijms23063126. [PMID: 35328546 PMCID: PMC8949970 DOI: 10.3390/ijms23063126] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/31/2022] Open
Abstract
Anemone coronaria L. (2n = 2x = 16) is a perennial, allogamous, highly heterozygous plant marketed as a cut flower or in gardens. Due to its large genome size, limited efforts have been made in order to develop species-specific molecular markers. We obtained the first draft genome of the species by Illumina sequencing an androgenetic haploid plant of the commercial line “MISTRAL® Magenta”. The genome assembly was obtained by applying the MEGAHIT pipeline and consisted of 2 × 106 scaffolds. The SciRoKo SSR (Simple Sequence Repeats)-search module identified 401.822 perfect and 188.987 imperfect microsatellites motifs. Following, we developed a user-friendly “Anemone coronaria Microsatellite DataBase” (AnCorDB), which incorporates the Primer3 script, making it possible to design couples of primers for downstream application of the identified SSR markers. Eight genotypes belonging to eight cultivars were used to validate 62 SSRs and a subset of markers was applied for fingerprinting each cultivar, as well as to assess their intra-cultivar variability. The newly developed microsatellite markers will find application in Breeding Rights disputes, developing genetic maps, marker assisted breeding (MAS) strategies, as well as phylogenetic studies.
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Comparative RNA-Seq profiling of a resistant and susceptible peanut ( Arachis hypogaea) genotypes in response to leaf rust infection caused by Puccinia arachidis. 3 Biotech 2020; 10:284. [PMID: 32550103 DOI: 10.1007/s13205-020-02270-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/20/2020] [Indexed: 10/24/2022] Open
Abstract
The goal of this study was to identify differentially expressed genes (DEGs) responsible for peanut plant (Arachis hypogaea) defence against Puccinia arachidis (causative agent of rust disease). Genes were identified using a high-throughput RNA-sequencing strategy. In total, 86,380,930 reads were generated from RNA-Seq data of two peanut genotypes, JL-24 (susceptible), and GPBD-4 (resistant). Gene Ontology (GO) and KEGG analysis of DEGs revealed essential genes and their pathways responsible for defence response to P. arachidis. DEGs uniquely upregulated in resistant genotype included pathogenesis-related (PR) proteins, MLO such as protein, ethylene-responsive factor, thaumatin, and F-box, whereas, other genes down-regulated in susceptible genotype were Caffeate O-methyltransferase, beta-glucosidase, and transcription factors (WRKY, bZIP, MYB). Moreover, various genes, such as Chitinase, Cytochrome P450, Glutathione S-transferase, and R genes such as NBS-LRR were highly up-regulated in the resistant genotype, indicating their involvement in the plant defence mechanism. RNA-Seq analysis data were validated by RT-qPCR using 15 primer sets derived from DEGs producing high correlation value (R 2 = 0.82). A total of 4511 EST-SSRs were identified from the unigenes, which can be useful in evaluating genetic diversity among genotypes, QTL mapping, and plant variety improvement through marker-assisted breeding. These findings will help to understand the molecular defence mechanisms of the peanut plant in response to P. arachidis infection.
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Qiu A, Lei Y, Yang S, Wu J, Li J, Bao B, Cai Y, Wang S, Lin J, Wang Y, Shen L, Cai J, Guan D, He S. CaC3H14 encoding a tandem CCCH zinc finger protein is directly targeted by CaWRKY40 and positively regulates the response of pepper to inoculation by Ralstonia solanacearum. MOLECULAR PLANT PATHOLOGY 2018; 19:2221-2235. [PMID: 29683552 PMCID: PMC6638151 DOI: 10.1111/mpp.12694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/27/2018] [Accepted: 04/20/2018] [Indexed: 05/10/2023]
Abstract
Tandem CCCH zinc finger (TZnF) proteins have been implicated in plant defence, but their role in pepper (Capsicum annuum) is unclear. In the present study, the role of CaC3H14, a pepper TZnF protein, in the immune response of pepper plants to Ralstonia solanacearum infection was characterized. When fused to the green fluorescent protein, CaC3H14 was localized exclusively to the nuclei in leaf cells of Nicotiana benthamiana plants transiently overexpressing CaC3H14. Transcript abundance of CaC3H14 was up-regulated by inoculation with R. solanacearum. Virus-induced silencing of CaC3H14 increased the susceptibility of the plants to R. solanacearum and down-regulated the genes associated with the hypersensitive response (HR), specifically HIR1 and salicylic acid (SA)-dependent PR1a. By contrast, silencing resulted in the up-regulation of jasmonic acid (JA)-dependent DEF1 and ethylene (ET) biosynthesis-associated ACO1. Transient overexpression of CaC3H14 in pepper triggered an intensive HR, indicated by cell death and hydrogen peroxide (H2 O2 ) accumulation, up-regulated PR1a and down-regulated DEF1 and ACO1. Ectopic overexpression of CaC3H14 in tobacco plants significantly decreased the susceptibility of tobacco plants to R. solanacearum. It also up-regulated HR-associated HSR515, immunity-associated GST1 and the SA-dependent marker genes NPR1 and PR2, but down-regulated JA-dependent PR1b and ET-dependent EFE26. The CaC3H14 promoter and was bound and its transcription was up-regulated by CaWRKY40. Collectively, these results indicate that CaC3H14 is transcriptionally targeted by CaWRKY40, is a modulator of the antagonistic interaction between SA and JA/ET signalling, and enhances the defence response of pepper plants to infection by R. solanacearum.
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Affiliation(s)
- Ailian Qiu
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Yufen Lei
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Sheng Yang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Ji Wu
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Jiazhi Li
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Bingjin Bao
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Yiting Cai
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Song Wang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Jinhui Lin
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Yuzhu Wang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Lei Shen
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Jinsen Cai
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Deyi Guan
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Shuilin He
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
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Goh KM, Dickinson M, Supramaniam CV. Morphological and transcript changes in the biosynthesis of lignin in oil palm (Elaeis guineensis) during Ganoderma boninense infections in vitro. PHYSIOLOGIA PLANTARUM 2018; 162:274-289. [PMID: 28940509 DOI: 10.1111/ppl.12645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/31/2017] [Accepted: 09/16/2017] [Indexed: 06/07/2023]
Abstract
Lignification of the plant cell wall could serve as the first line of defense against pathogen attack, but the molecular mechanisms of virulence and disease between oil palm and Ganoderma boninense are poorly understood. This study presents the biochemical, histochemical, enzymology and gene expression evidences of enhanced lignin biosynthesis in young oil palm as a response to G. boninense (GBLS strain). Comparative studies with control (T1), wounded (T2) and infected (T3) oil palm plantlets showed significant accumulation of total lignin content and monolignol derivatives (syringaldehyde and vanillin). These derivatives were deposited on the epidermal cell wall of infected plants. Moreover, substantial differences were detected in the activities of enzyme and relative expressions of genes encoding phenylalanine ammonia lyase (EC 4.3.1.24), cinnamate 4-hydroxylase (EC 1.14.13.11), caffeic acid O-methyltransferase (EC 2.1.1.68) and cinnamyl alcohol dehydrogenase (CAD, EC 1.1.1.195). These enzymes are key intermediates dedicated to the biosynthesis of lignin monomers, the guaicyl (G), syringyl (S) and ρ-hydroxyphenyl (H) subunits. Results confirmed an early, biphasic and transient positive induction of all gene intermediates, except for CAD enzyme activities. These differences were visualized by anatomical and metabolic changes in the profile of lignin in the oil palm plantlets such as low G lignin, indicating a potential mechanism for enhanced susceptibility toward G. boninense infection.
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Affiliation(s)
- Kar Mun Goh
- School of Biosciences, Faculty of Sciences, The University of Nottingham Malaysia Campus, 43500, Semenyih, Malaysia
| | - Matthew Dickinson
- School of Biosciences, The University of Nottingham Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Christina V Supramaniam
- School of Biosciences, Faculty of Sciences, The University of Nottingham Malaysia Campus, 43500, Semenyih, Malaysia
- Centre of Sustainable Palm Oil Research (CESPOR), The University of Nottingham Malaysia Campus, 43500, Semenyih, Malaysia
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Ayala-Sumuano JT, Licea-Navarro A, Rudiño-Piñera E, Rodríguez E, Rodríguez-Almazán C. Sequencing and de novo transcriptome assembly of Anthopleura dowii Verrill (1869), from Mexico. GENOMICS DATA 2017; 11:92-94. [PMID: 28066713 PMCID: PMC5200871 DOI: 10.1016/j.gdata.2016.11.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 11/18/2016] [Indexed: 11/30/2022]
Abstract
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Moreover, the development of tools for big data set analysis has allowed the identification of molecules and networks involved in metabolism, evolution or behavior. By natural habitats aquatic organisms have implemented molecular strategies for survival, including the production and secretion of toxic compounds for their predators; therefore these organisms are possible sources of proteins or peptides with potential biotechnological application. In the last decade anthozoans, mainly octocorals but also sea anemones, have been proben to be a source of natural products. Members of the genus Anthopleura are one of the best known and most studied sea anemones because they are common constituents of rocky intertidal communities and show interesting ecological and biological phenomena (e.g. intraespecific competition, symbiosis, etc.); however, many aspects of these taxa remain in need to be analyzed. This work describes the transcriptome sequencing of Anthopleura dowii Verrill, 1869 (Cnidaria: Anthozoa: Actiniaria); this is the first report of this kind for these species. The data set used to construct the transcriptome has been deposited on NCBI's database. Illumina sequence reads are available under BioProject accession number PRJNA329297 and Sequence Read Archive under accession number SRP078992.
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Affiliation(s)
- Jorge-Tonatiuh Ayala-Sumuano
- Instituto de Neurobilogía, Universidad Nacional Autónoma de México, Blvd. Juriquilla 30001, Juriquilla, Querétaro, México
| | - Alexei Licea-Navarro
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Baja California, C.P. 22860, México
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, C.P. 62210, Cuernavaca, Morelos, México
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York NY 10024, USA
| | - Claudia Rodríguez-Almazán
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, C.P. 62210, Cuernavaca, Morelos, México
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Hao DC, Gu X, Xiao P. Anemone medicinal plants: ethnopharmacology, phytochemistry and biology. Acta Pharm Sin B 2017; 7:146-158. [PMID: 28303220 PMCID: PMC5343163 DOI: 10.1016/j.apsb.2016.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/12/2022] Open
Abstract
The Ranunculaceae genus Anemone (order Ranunculales), comprising more than 150 species, mostly herbs, has long been used in folk medicine and worldwide ethnomedicine. Various medicinal compounds have been found in Anemone plants, especially triterpenoid saponins, some of which have shown anti-cancer activities. Some Anemone compounds and extracts display immunomodulatory, anti-inflammatory, antioxidant, and antimicrobial activities. More than 50 species have ethnopharmacological uses, which provide clues for modern drug discovery. Anemone compounds exert anticancer and other bioactivities via multiple pathways. However, a comprehensive review of the Anemone medicinal resources is lacking. We here summarize the ethnomedical knowledge and recent progress on the chemical and pharmacological diversity of Anemone medicinal plants, as well as the emerging molecular mechanisms and functions of these medicinal compounds. The phylogenetic relationships of Anemone species were reconstructed based on nuclear ITS and chloroplast markers. The molecular phylogeny is largely congruent with the morphology-based classification. Commonly used medicinal herbs are distributed in each subgenus and section, and chemical and biological studies of more unexplored taxa are warranted. Gene expression profiling and relevant "omics" platforms could reveal differential effects of phytometabolites. Genomics, transcriptomics, proteomics, and metabolomics should be highlighted in deciphering novel therapeutic mechanisms and utilities of Anemone phytometabolites.
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Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian 116028, China
| | - Xiaojie Gu
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian 116028, China
| | - Peigen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
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Khaksar G, Sayed Tabatabaei BE, Arzani A, Ghobadi C, Ebrahimie E. Functional Analysis of a Pomegranate ( Punica granatum L.) MYB Transcription Factor Involved in the Regulation of Anthocyanin Biosynthesis. IRANIAN JOURNAL OF BIOTECHNOLOGY 2015; 13:17-25. [PMID: 28959277 DOI: 10.15171/ijb.1045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
BACKGROUND Pomegranate fruit (Punica granatum L.) is a rich source of anthocyanin pigments resulting in vibrant colours and anti-oxidant contents. Although the intensity and pattern of anthocyanin biosynthesis in fruit are strongly influenced by R2R3-MYB transcription factors, little is known about the regulation and role of MYB in anthocyanin pathway of pomegranate. OBJECTIVES The present study was conducted to elucidate the relationship between the expression of MYB transcription factor and the anthocyanin accumulation during the colour development phase of pomegranate fruits. MATERIALS AND METHODS In this work, R2R3-MYB transcription factor (PgMYB) was isolated and characterized from pomegranate skin through RACE-PCR. The expression of PgMYB gene was monitored in three distinct pomegranate accessions with distinctive skin colour and pattern by semi-quantitative RT-PCR. RESULTS The results indicated a strong association between skin colour in mature pomegranate fruits with the PgMYB transcripts. The highest expression level of PgMYB gene was observed in Poost Siyah Yazd (dark purple skin) throughout the ripening process. Furthermore, comparison of PgMYB amino acid sequences with those of R2R3-MYB family in grapevine, eucalyptus, peach, cacao, populus and Arabidopsis demonstrated that this protein shares high similarity (75-85% amino acid identity) with their conserved MYB domain. Computational structure prediction of PgMYB showed that the three conserved amino acids (Asn, Lys and Lys) are present in the same position of the MYB domain. CONCLUSIONS It is speculated that PgMYB gene influences the fruit colour and could be used to improve the accumula-tion of anthocyanin pigments in the pomegranate fruit.
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Affiliation(s)
- Ghazale Khaksar
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Badraldin Ebrahim Sayed Tabatabaei
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.,Department of Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584CH, Utrecht , The Netherlands
| | - Ahmad Arzani
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Cyrus Ghobadi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Esmaeil Ebrahimie
- Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, 73761, Iran.,Discipline of Genetics, School of Biological Science, University of Adelaide, Adelaide, 5001, SA, Australia
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